Zinc in PDB 8jws: Ephd Domain of Phd Finger Protein 7 (PHF7)
Protein crystallography data
The structure of Ephd Domain of Phd Finger Protein 7 (PHF7), PDB code: 8jws
was solved by
I.Bang,
H.S.Lee,
H.-J.Choi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
31.01 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
37.014,
59.145,
170.396,
90,
90,
90
|
R / Rfree (%)
|
19.7 /
22.3
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Ephd Domain of Phd Finger Protein 7 (PHF7)
(pdb code 8jws). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the
Ephd Domain of Phd Finger Protein 7 (PHF7), PDB code: 8jws:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Zinc binding site 1 out
of 9 in 8jws
Go back to
Zinc Binding Sites List in 8jws
Zinc binding site 1 out
of 9 in the Ephd Domain of Phd Finger Protein 7 (PHF7)
![](/pictures/ZN/pdb/jw/8jws-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/jw/8jws-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Ephd Domain of Phd Finger Protein 7 (PHF7) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn501
b:13.1
occ:0.97
|
ND1
|
A:HIS58
|
2.1
|
9.3
|
1.0
|
SG
|
A:CYS36
|
2.3
|
13.3
|
1.0
|
SG
|
A:CYS61
|
2.3
|
12.4
|
1.0
|
SG
|
A:CYS33
|
2.4
|
11.3
|
1.0
|
CE1
|
A:HIS58
|
3.0
|
12.5
|
1.0
|
CB
|
A:CYS33
|
3.0
|
10.0
|
1.0
|
CG
|
A:HIS58
|
3.1
|
12.8
|
1.0
|
CB
|
A:CYS36
|
3.2
|
15.0
|
1.0
|
CB
|
A:CYS61
|
3.3
|
13.0
|
1.0
|
CB
|
A:HIS58
|
3.4
|
12.0
|
1.0
|
N
|
A:CYS36
|
3.7
|
13.5
|
1.0
|
CA
|
A:CYS36
|
4.0
|
16.7
|
1.0
|
N
|
A:HIS58
|
4.1
|
8.9
|
1.0
|
NE2
|
A:HIS58
|
4.1
|
15.8
|
1.0
|
CD2
|
A:HIS58
|
4.2
|
13.1
|
1.0
|
CA
|
A:HIS58
|
4.4
|
12.5
|
1.0
|
CA
|
A:CYS33
|
4.5
|
12.0
|
1.0
|
CA
|
A:CYS61
|
4.7
|
14.4
|
1.0
|
C
|
A:LEU35
|
4.8
|
16.3
|
1.0
|
C
|
A:CYS36
|
4.8
|
15.7
|
1.0
|
CB
|
A:LEU35
|
4.9
|
12.1
|
1.0
|
O
|
A:HOH694
|
4.9
|
14.0
|
1.0
|
|
Zinc binding site 2 out
of 9 in 8jws
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Zinc Binding Sites List in 8jws
Zinc binding site 2 out
of 9 in the Ephd Domain of Phd Finger Protein 7 (PHF7)
![](/pictures/ZN/pdb/jw/8jws-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/jw/8jws-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Ephd Domain of Phd Finger Protein 7 (PHF7) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn502
b:15.4
occ:0.95
|
ND1
|
A:HIS120
|
2.1
|
15.1
|
1.0
|
SG
|
A:CYS101
|
2.3
|
17.3
|
1.0
|
SG
|
A:CYS123
|
2.3
|
16.0
|
1.0
|
SG
|
A:CYS98
|
2.4
|
13.0
|
1.0
|
CE1
|
A:HIS120
|
3.0
|
14.4
|
1.0
|
CB
|
A:CYS98
|
3.1
|
14.5
|
1.0
|
CG
|
A:HIS120
|
3.2
|
12.3
|
1.0
|
CB
|
A:CYS123
|
3.2
|
12.9
|
1.0
|
CB
|
A:CYS101
|
3.4
|
19.3
|
1.0
|
O
|
A:HOH710
|
3.5
|
32.2
|
1.0
|
CB
|
A:HIS120
|
3.6
|
12.9
|
1.0
|
N
|
A:CYS101
|
3.8
|
18.9
|
1.0
|
N
|
A:HIS120
|
4.1
|
16.2
|
1.0
|
NE2
|
A:HIS120
|
4.2
|
13.5
|
1.0
|
CA
|
A:CYS101
|
4.2
|
20.6
|
1.0
|
CD2
|
A:HIS120
|
4.3
|
13.9
|
1.0
|
CA
|
A:HIS120
|
4.5
|
12.6
|
1.0
|
CA
|
A:CYS98
|
4.5
|
15.8
|
1.0
|
CB
|
A:VAL100
|
4.7
|
16.9
|
1.0
|
CA
|
A:CYS123
|
4.7
|
19.0
|
1.0
|
O
|
A:HOH697
|
4.8
|
23.8
|
1.0
|
C
|
A:VAL100
|
4.9
|
17.2
|
1.0
|
C
|
A:CYS101
|
5.0
|
22.0
|
1.0
|
O
|
A:HIS120
|
5.0
|
10.2
|
1.0
|
|
Zinc binding site 3 out
of 9 in 8jws
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Zinc Binding Sites List in 8jws
Zinc binding site 3 out
of 9 in the Ephd Domain of Phd Finger Protein 7 (PHF7)
![](/pictures/ZN/pdb/jw/8jws-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/jw/8jws-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Ephd Domain of Phd Finger Protein 7 (PHF7) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn503
b:16.8
occ:0.99
|
ND1
|
A:HIS144
|
2.0
|
24.8
|
1.0
|
SG
|
A:CYS110
|
2.3
|
15.5
|
1.0
|
SG
|
A:CYS115
|
2.4
|
17.0
|
1.0
|
SG
|
A:CYS141
|
2.5
|
23.6
|
1.0
|
CE1
|
A:HIS144
|
2.9
|
27.8
|
1.0
|
CG
|
A:HIS144
|
3.0
|
23.7
|
1.0
|
CB
|
A:CYS115
|
3.2
|
23.1
|
1.0
|
CB
|
A:CYS110
|
3.2
|
12.1
|
1.0
|
CB
|
A:CYS141
|
3.3
|
23.0
|
1.0
|
CB
|
A:HIS144
|
3.5
|
20.9
|
1.0
|
N
|
A:CYS141
|
3.9
|
18.3
|
1.0
|
NE2
|
A:HIS144
|
4.0
|
26.3
|
1.0
|
CD2
|
A:HIS144
|
4.1
|
27.0
|
1.0
|
CA
|
A:CYS141
|
4.1
|
16.2
|
1.0
|
CG
|
A:LYS143
|
4.4
|
44.3
|
1.0
|
CB
|
A:ASN112
|
4.5
|
17.2
|
1.0
|
N
|
A:HIS144
|
4.6
|
26.3
|
1.0
|
CG
|
A:GLN117
|
4.6
|
23.5
|
1.0
|
CA
|
A:CYS115
|
4.6
|
19.5
|
1.0
|
CA
|
A:CYS110
|
4.7
|
12.2
|
1.0
|
CA
|
A:HIS144
|
4.7
|
26.1
|
1.0
|
CB
|
A:GLN117
|
4.7
|
15.6
|
1.0
|
C
|
A:CYS141
|
4.8
|
23.4
|
1.0
|
O
|
A:CYS141
|
4.9
|
23.3
|
1.0
|
O
|
A:HOH706
|
5.0
|
38.2
|
1.0
|
CD
|
A:LYS143
|
5.0
|
43.4
|
1.0
|
|
Zinc binding site 4 out
of 9 in 8jws
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Zinc Binding Sites List in 8jws
Zinc binding site 4 out
of 9 in the Ephd Domain of Phd Finger Protein 7 (PHF7)
![](/pictures/ZN/pdb/jw/8jws-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/jw/8jws-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Ephd Domain of Phd Finger Protein 7 (PHF7) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn501
b:19.0
occ:1.00
|
ND1
|
B:HIS58
|
2.1
|
18.1
|
1.0
|
SG
|
B:CYS36
|
2.3
|
19.0
|
1.0
|
SG
|
B:CYS61
|
2.3
|
20.4
|
1.0
|
SG
|
B:CYS33
|
2.4
|
18.9
|
1.0
|
CB
|
B:CYS33
|
3.1
|
16.9
|
1.0
|
CE1
|
B:HIS58
|
3.1
|
21.6
|
1.0
|
CG
|
B:HIS58
|
3.1
|
18.8
|
1.0
|
CB
|
B:CYS36
|
3.1
|
16.6
|
1.0
|
CB
|
B:CYS61
|
3.3
|
17.9
|
1.0
|
CB
|
B:HIS58
|
3.4
|
15.5
|
1.0
|
N
|
B:CYS36
|
3.7
|
20.4
|
1.0
|
CA
|
B:CYS36
|
4.0
|
23.1
|
1.0
|
N
|
B:HIS58
|
4.2
|
15.0
|
1.0
|
NE2
|
B:HIS58
|
4.2
|
19.7
|
1.0
|
CD2
|
B:HIS58
|
4.2
|
19.7
|
1.0
|
CA
|
B:HIS58
|
4.4
|
14.6
|
1.0
|
CA
|
B:CYS33
|
4.5
|
22.4
|
1.0
|
O
|
B:HOH692
|
4.7
|
15.7
|
1.0
|
CA
|
B:CYS61
|
4.7
|
16.7
|
1.0
|
C
|
B:LEU35
|
4.8
|
20.8
|
1.0
|
C
|
B:CYS36
|
4.8
|
26.5
|
1.0
|
CB
|
B:LEU35
|
4.9
|
20.2
|
1.0
|
N
|
B:LEU37
|
5.0
|
28.1
|
1.0
|
|
Zinc binding site 5 out
of 9 in 8jws
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Zinc Binding Sites List in 8jws
Zinc binding site 5 out
of 9 in the Ephd Domain of Phd Finger Protein 7 (PHF7)
![](/pictures/ZN/pdb/jw/8jws-ZN-sphere_05.jpg) Mono view
![](/pictures/ZN/pdb/jw/8jws-ZN-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Ephd Domain of Phd Finger Protein 7 (PHF7) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn502
b:24.9
occ:1.00
|
ND1
|
B:HIS120
|
2.2
|
27.5
|
1.0
|
SG
|
B:CYS101
|
2.3
|
26.9
|
1.0
|
SG
|
B:CYS123
|
2.3
|
30.6
|
1.0
|
SG
|
B:CYS98
|
2.3
|
22.8
|
1.0
|
CB
|
B:CYS98
|
3.1
|
21.3
|
1.0
|
CE1
|
B:HIS120
|
3.1
|
23.5
|
1.0
|
CB
|
B:CYS123
|
3.2
|
25.9
|
1.0
|
CG
|
B:HIS120
|
3.2
|
24.5
|
1.0
|
CB
|
B:CYS101
|
3.4
|
33.3
|
1.0
|
CB
|
B:HIS120
|
3.5
|
24.4
|
1.0
|
N
|
B:CYS101
|
3.9
|
28.7
|
1.0
|
N
|
B:HIS120
|
4.1
|
19.2
|
1.0
|
CA
|
B:CYS101
|
4.2
|
32.2
|
1.0
|
NE2
|
B:HIS120
|
4.2
|
21.4
|
1.0
|
CD2
|
B:HIS120
|
4.3
|
20.3
|
1.0
|
CA
|
B:HIS120
|
4.4
|
18.8
|
1.0
|
CA
|
B:CYS98
|
4.5
|
25.8
|
1.0
|
CA
|
B:CYS123
|
4.6
|
29.5
|
1.0
|
CB
|
B:VAL100
|
4.7
|
30.0
|
1.0
|
O
|
B:HIS120
|
4.9
|
21.0
|
1.0
|
O
|
B:HOH698
|
5.0
|
39.8
|
1.0
|
C
|
B:CYS101
|
5.0
|
34.2
|
1.0
|
C
|
B:VAL100
|
5.0
|
36.1
|
1.0
|
|
Zinc binding site 6 out
of 9 in 8jws
Go back to
Zinc Binding Sites List in 8jws
Zinc binding site 6 out
of 9 in the Ephd Domain of Phd Finger Protein 7 (PHF7)
![](/pictures/ZN/pdb/jw/8jws-ZN-sphere_06.jpg) Mono view
![](/pictures/ZN/pdb/jw/8jws-ZN-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Ephd Domain of Phd Finger Protein 7 (PHF7) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn503
b:18.9
occ:0.94
|
ND1
|
B:HIS144
|
2.1
|
21.8
|
1.0
|
SG
|
B:CYS115
|
2.3
|
20.9
|
1.0
|
SG
|
B:CYS141
|
2.3
|
26.2
|
1.0
|
SG
|
B:CYS110
|
2.3
|
18.5
|
1.0
|
CE1
|
B:HIS144
|
3.0
|
30.9
|
1.0
|
CG
|
B:HIS144
|
3.2
|
24.0
|
1.0
|
CB
|
B:CYS115
|
3.2
|
25.2
|
1.0
|
CB
|
B:CYS110
|
3.2
|
17.3
|
1.0
|
CB
|
B:CYS141
|
3.5
|
24.6
|
1.0
|
CB
|
B:HIS144
|
3.5
|
25.8
|
1.0
|
N
|
B:CYS141
|
4.0
|
21.4
|
1.0
|
NE2
|
B:HIS144
|
4.2
|
27.4
|
1.0
|
CD2
|
B:HIS144
|
4.2
|
26.5
|
1.0
|
CA
|
B:CYS141
|
4.3
|
23.0
|
1.0
|
CG
|
B:GLN117
|
4.6
|
27.4
|
1.0
|
CB
|
B:ASN112
|
4.6
|
19.8
|
1.0
|
CA
|
B:CYS115
|
4.6
|
22.6
|
1.0
|
CA
|
B:CYS110
|
4.7
|
16.1
|
1.0
|
CB
|
B:GLN117
|
4.7
|
20.9
|
1.0
|
N
|
B:HIS144
|
4.7
|
30.7
|
1.0
|
CG
|
B:LYS143
|
4.8
|
47.7
|
1.0
|
CA
|
B:HIS144
|
4.8
|
30.6
|
1.0
|
C
|
B:CYS141
|
4.8
|
29.0
|
1.0
|
O
|
B:CYS141
|
4.9
|
25.8
|
1.0
|
|
Zinc binding site 7 out
of 9 in 8jws
Go back to
Zinc Binding Sites List in 8jws
Zinc binding site 7 out
of 9 in the Ephd Domain of Phd Finger Protein 7 (PHF7)
![](/pictures/ZN/pdb/jw/8jws-ZN-sphere_07.jpg) Mono view
![](/pictures/ZN/pdb/jw/8jws-ZN-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Ephd Domain of Phd Finger Protein 7 (PHF7) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn501
b:19.3
occ:0.99
|
ND1
|
C:HIS58
|
2.1
|
19.2
|
1.0
|
SG
|
C:CYS61
|
2.3
|
17.9
|
1.0
|
SG
|
C:CYS36
|
2.3
|
22.2
|
1.0
|
SG
|
C:CYS33
|
2.4
|
19.4
|
1.0
|
CB
|
C:CYS33
|
3.0
|
21.7
|
1.0
|
CE1
|
C:HIS58
|
3.1
|
17.3
|
1.0
|
CG
|
C:HIS58
|
3.1
|
15.5
|
1.0
|
CB
|
C:CYS36
|
3.2
|
19.7
|
1.0
|
CB
|
C:CYS61
|
3.3
|
13.4
|
1.0
|
CB
|
C:HIS58
|
3.5
|
14.5
|
1.0
|
N
|
C:CYS36
|
3.7
|
21.3
|
1.0
|
CA
|
C:CYS36
|
4.0
|
23.3
|
1.0
|
N
|
C:HIS58
|
4.2
|
14.7
|
1.0
|
NE2
|
C:HIS58
|
4.2
|
19.4
|
1.0
|
CD2
|
C:HIS58
|
4.2
|
16.3
|
1.0
|
CA
|
C:HIS58
|
4.4
|
15.2
|
1.0
|
CA
|
C:CYS33
|
4.5
|
21.2
|
1.0
|
CA
|
C:CYS61
|
4.7
|
14.7
|
1.0
|
C
|
C:LEU35
|
4.7
|
23.5
|
1.0
|
C
|
C:CYS36
|
4.8
|
31.9
|
1.0
|
O
|
C:HOH652
|
4.8
|
15.5
|
1.0
|
CB
|
C:LEU35
|
4.8
|
17.8
|
1.0
|
N
|
C:LEU37
|
5.0
|
26.7
|
1.0
|
|
Zinc binding site 8 out
of 9 in 8jws
Go back to
Zinc Binding Sites List in 8jws
Zinc binding site 8 out
of 9 in the Ephd Domain of Phd Finger Protein 7 (PHF7)
![](/pictures/ZN/pdb/jw/8jws-ZN-sphere_08.jpg) Mono view
![](/pictures/ZN/pdb/jw/8jws-ZN-sphere_08_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Ephd Domain of Phd Finger Protein 7 (PHF7) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn502
b:29.8
occ:0.95
|
ND1
|
C:HIS120
|
2.1
|
26.9
|
1.0
|
SG
|
C:CYS123
|
2.3
|
30.7
|
1.0
|
SG
|
C:CYS101
|
2.3
|
34.0
|
1.0
|
SG
|
C:CYS98
|
2.3
|
23.7
|
1.0
|
CB
|
C:CYS98
|
3.0
|
25.6
|
1.0
|
CE1
|
C:HIS120
|
3.1
|
28.8
|
1.0
|
CG
|
C:HIS120
|
3.2
|
19.8
|
1.0
|
CB
|
C:CYS123
|
3.2
|
29.1
|
1.0
|
CB
|
C:CYS101
|
3.4
|
34.3
|
1.0
|
CB
|
C:HIS120
|
3.5
|
22.3
|
1.0
|
N
|
C:CYS101
|
3.8
|
36.0
|
1.0
|
N
|
C:HIS120
|
4.1
|
19.9
|
1.0
|
CA
|
C:CYS101
|
4.2
|
29.7
|
1.0
|
NE2
|
C:HIS120
|
4.2
|
26.0
|
1.0
|
CD2
|
C:HIS120
|
4.3
|
19.9
|
1.0
|
CA
|
C:HIS120
|
4.4
|
21.6
|
1.0
|
CA
|
C:CYS98
|
4.5
|
27.2
|
1.0
|
CA
|
C:CYS123
|
4.7
|
28.4
|
1.0
|
CB
|
C:VAL100
|
4.7
|
36.6
|
1.0
|
C
|
C:VAL100
|
4.9
|
38.0
|
1.0
|
C
|
C:CYS101
|
5.0
|
36.8
|
1.0
|
O
|
C:HIS120
|
5.0
|
19.6
|
1.0
|
|
Zinc binding site 9 out
of 9 in 8jws
Go back to
Zinc Binding Sites List in 8jws
Zinc binding site 9 out
of 9 in the Ephd Domain of Phd Finger Protein 7 (PHF7)
![](/pictures/ZN/pdb/jw/8jws-ZN-sphere_09.jpg) Mono view
![](/pictures/ZN/pdb/jw/8jws-ZN-sphere_09_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Ephd Domain of Phd Finger Protein 7 (PHF7) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn503
b:19.9
occ:0.95
|
ND1
|
C:HIS144
|
2.1
|
27.8
|
1.0
|
SG
|
C:CYS141
|
2.3
|
22.6
|
1.0
|
SG
|
C:CYS115
|
2.4
|
22.8
|
1.0
|
SG
|
C:CYS110
|
2.4
|
22.8
|
1.0
|
CE1
|
C:HIS144
|
3.1
|
27.7
|
1.0
|
CB
|
C:CYS110
|
3.1
|
18.9
|
1.0
|
CG
|
C:HIS144
|
3.2
|
29.7
|
1.0
|
CB
|
C:CYS115
|
3.2
|
25.4
|
1.0
|
CB
|
C:CYS141
|
3.4
|
21.6
|
1.0
|
CB
|
C:HIS144
|
3.5
|
25.9
|
1.0
|
N
|
C:CYS141
|
4.0
|
23.0
|
1.0
|
NE2
|
C:HIS144
|
4.2
|
28.1
|
1.0
|
CA
|
C:CYS141
|
4.2
|
20.8
|
1.0
|
CD2
|
C:HIS144
|
4.3
|
31.9
|
1.0
|
CG
|
C:GLN117
|
4.5
|
28.1
|
1.0
|
CB
|
C:ASN112
|
4.6
|
21.8
|
1.0
|
CA
|
C:CYS110
|
4.6
|
17.8
|
1.0
|
CB
|
C:GLN117
|
4.6
|
25.5
|
1.0
|
CA
|
C:CYS115
|
4.7
|
27.2
|
1.0
|
N
|
C:HIS144
|
4.7
|
25.3
|
1.0
|
CA
|
C:HIS144
|
4.8
|
30.7
|
1.0
|
C
|
C:CYS141
|
4.8
|
20.8
|
1.0
|
CG
|
C:LYS143
|
4.8
|
45.1
|
1.0
|
O
|
C:CYS141
|
4.9
|
18.9
|
1.0
|
|
Reference:
H.S.Lee,
I.Bang,
J.You,
T.K.Jeong,
C.R.Kim,
M.Hwang,
J.S.Kim,
S.H.Baek,
J.J.Song,
H.J.Choi.
Molecular Basis For PHF7-Mediated Ubiquitination of Histone H3. Genes Dev. 2023.
ISSN: ISSN 0890-9369
PubMed: 37993255
DOI: 10.1101/GAD.350989.123
Page generated: Thu Dec 28 13:22:42 2023
|